Rational Design of Robust Biomolecular Circuits : from Specification to Parameters

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2011
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Hafner, Marc
Lu, James
Koeppl, Heinz
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KOEPPL, Heinz, ed. and others. Design and analysis of biomolecular circuits : engineering approaches to systems and synthetic biology. New York, NY: Springer, 2011, pp. 253-279. ISBN 978-1-4419-6765-7. Available under: doi: 10.1007/978-1-4419-6766-4_12
Zusammenfassung

Despite the early success stories synthetic biology, the development of larger, more complex synthetic systems necessitates the use of appropriate design methodologies. In particular, the integration of smaller circuits in order to perform complex tasks remains one of the most important challenges faced in synthetic biology. We propose here a methodology to determine the region in the parameter space where a given dynamical model works as desired. It is based on the inverse problem of finding parameter sets that exhibit the specified behavior for a defined topology. The main issue we face is that such inverse mapping is highly expansive and suffers from instability: small changes in the specified dynamic property could lead to large deviations in the parameters for the identified models. To solve this issue, we discuss regularized maps complemented by local analysis. With a stabilized inversion map, small neighborhoods in the property space are mapped to small neighborhoods in the parameter space, thereby finding parameter vectors that are robust to the problem specification. To specify dynamic circuit properties we discuss Linear Temporal Logic (LTL). We apply these concepts to two models of the cyanobacterial circadian oscillation.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
004 Informatik
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Robustness, Inverse problems, Robust control, Optimal control, Circuit design, Formal verification
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ISO 690HAFNER, Marc, Tatjana PETROV, James LU, Heinz KOEPPL, 2011. Rational Design of Robust Biomolecular Circuits : from Specification to Parameters. In: KOEPPL, Heinz, ed. and others. Design and analysis of biomolecular circuits : engineering approaches to systems and synthetic biology. New York, NY: Springer, 2011, pp. 253-279. ISBN 978-1-4419-6765-7. Available under: doi: 10.1007/978-1-4419-6766-4_12
BibTex
@incollection{Hafner2011Ratio-42104,
  year={2011},
  doi={10.1007/978-1-4419-6766-4_12},
  title={Rational Design of Robust Biomolecular Circuits : from Specification to Parameters},
  isbn={978-1-4419-6765-7},
  publisher={Springer},
  address={New York, NY},
  booktitle={Design and analysis of biomolecular circuits : engineering approaches to systems and synthetic biology},
  pages={253--279},
  editor={Koeppl, Heinz},
  author={Hafner, Marc and Petrov, Tatjana and Lu, James and Koeppl, Heinz}
}
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